Diane L. Rowland

Gene expression profiling in peanut using high density oligonucleotide microarrays

BackgroundTranscriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently has a significant number of ESTs been released into the public domain. Utilization of these ESTs for oligonucleotide microarrays provides a means to investigate large-scale transcript responses to a variety of developmental and environmental signals, ultimately improving our understanding of plant biology.ResultsWe have developed a high-density oligonucleotide microarray for peanut using 49,205 publicly available ESTs and tested the utility of this array for expression profiling in a variety of peanut tissues. To identify putatively tissue-specific genes and demonstrate the utility of this array for expression profiling in a variety of peanut tissues, we compared transcript levels in pod, peg, leaf, stem, and root tissues. Results from this experiment showed 108 putatively pod-specific/abundant genes, as well as transcripts whose expression was low or undetected in pod compared to peg, leaf, stem, or root. The transcripts significantly over-represented in pod include genes responsible for seed storage proteins and desiccation (e.g., late-embryogenesis abundant proteins, aquaporins, legumin B), oil production, and cellular defense. Additionally, almost half of the pod-abundant genes represent unknown genes allowing for the possibility of associating putative function to these previously uncharacterized genes.ConclusionThe peanut oligonucleotide array represents the majority of publicly available peanut ESTs and can be used as a tool for expression profiling studies in diverse tissues.

Determination of Maturity and Degree Day Indices and their Success in Predicting Peanut Maturity1

Abstract The ability to accurately assess and predict peanut maturity is a strong determinant of the economic return to the producer as it governs crop quality, flavor, and yield. However, the currently available methods used to predict peanut maturity are based on hull color determination and are somewhat labor-intensive and subject to the observers ability to finely discriminate color classes. The objectives in this study were: 1) create an index of maturity based on the distribution of peanut pods within the accepted maturity profile board classes that give the best quantifiable correlation with peanut yield, grade, and net value; and 2) test degree day models to determine their efficacy in predicting the optimum maturity index. Peanuts were harvested on 7 and 6 sequential dates in 2003 and 2004, respectively, at two sites in southwest Georgia, USA. Several maturity indices were calculated at each harvest based on the percentage of pods in each color class of the maturity profile board. For both sites...

Shotgun label-free quantitative proteomics of water-deficit-stressed midmature peanut (Arachis hypogaea L.) seed.

Legume seeds and peanuts, in particular, are an inexpensive source of plant proteins and edible oil. A comprehensive understanding of seed metabolism and the effects of water-deficit stress on the incorporation of the main storage reserves in seeds, such as proteins, fatty acids, starch, and secondary metabolites, will enhance our ability to improve seed quality and yield through molecular breeding programs. In the present study, we employed a label-free quantitative proteomics approach to study the functional proteins altered in the midmature (65-70 days postanthesis) peanut seed grown under water-deficit stress conditions. We created a pod-specific proteome database and identified 93 nonredundant, statistically significant, and differentially expressed proteins between well-watered and drought-stressed seeds. Mapping of these differential proteins revealed three candidate biological pathways (glycolysis, sucrose and starch metabolism, and fatty acid metabolism) that were significantly altered due to water-deficit stress. Differential accumulation of proteins from these pathways provides insight into the molecular mechanisms underlying the observed physiological changes, which include reductions in pod yield and biomass, reduced germination, reduced vigor, decreased seed membrane integrity, increase in storage proteins, and decreased total fatty acid content. Some of the proteins encoding rate limiting enzymes of biosynthetic pathways could be utilized by breeders to improve peanut seed production during water-deficit conditions in the field. The data have been deposited to the ProteomeXchange with identifier PXD000308.

Economic Returns of Irrigated and Non-Irrigated Peanut Based Cropping Systems

Proper crop rotation is essential to maintaining high peanut yield and quality. However, the economic considerations of sustainable cropping systems must incorporate commodity prices, production costs, and yield responses of the crops within the cropping system. Research was conducted at the USDA/ARS National Peanut Research Laboratorys Multi-crop Irrigation Research Farm in Shellman, Georgia to determine the average net returns of irrigated and non-irrigated cropping systems consisting of peanut (Arachis hypogea L.), cotton (Gossypium hirsutum L.), and corn (Zea mays L.). Five replicated cropping systems provided data on yield responses from irrigated and non-irrigated rotation sequences defined as: continuous peanuts (PPP), cotton/peanuts/cotton (CPC), corn/peanuts/corn (MPM), cotton/cotton/peanuts (CCP), and cotton/corn/peanuts (CMP). The peanut yield in the PPP rotation was 3300 kg/ha in the non-irrigated treatment. Non-irrigated yields in CPC and MPM rotation sequences were 3940 and 3890 kg/ha, respectively and yields in CCP and CMP rotation sequences were 4770 and 4710 kg/ha, respectively. The peanut yield in the PPP rotation was 4080 kg/ha in the irrigated treatment. Irrigated yields in CPC and MPM rotation sequences were 5280 and 5230 kg/ha, respectively and yields in CCP and CMP rotation sequences were 5940 and 6010 kg/ha, respectively. The economic returns of the cropping systems were analyzed for 3 different price level combinations. Production costs (variable and fixed) were obtained from partial budgets. Returns were defined as the 3 year average net returns of each cropping system and were calculated for each price level combination which resulted in 57 comparable average net returns for the irrigated and non-irrigated treatments. Net returns were influenced by rotation sequence, price, and irrigation.

Five Years of Subsurface Drip Irrigation on Peanut: What Have We Learned?1

Abstract Long term peanut yield with various crop rotations and irrigated with subsurface drip irrigation (SDI) is not known. A subsurface drip irrigation system was installed in 1998 on a Tifton loamy sand (Fine-loamy, kaolinitic, thermic Plinthic Kandiudults) with five crop rotations, two drip tube lateral spacings, and three irrigation levels. Crop rotations ranged from continuous peanut (Arachis hypogaea L.) to four years between peanut rotated with either cotton (Gossypium hirusutum L.) and/or corn (Zea mays L.). Laterals were installed underneath each crop row (narrow) and alternate row middles (wide). Crops were irrigated daily at 100, 75 and 50% of estimated crop water use. Continuous peanut yields averaged 3107 kg ha−1 while peanut in rotation averaged 4031 kg ha−1. Yield of peanut in any rotation and with narrow spaced drip tube laterals averaged 4883 kg ha−1 and wide spaced laterals averaged 4592 kg ha−1. Peanut in any rotation and irrigated at 75% had the same pod yield as the 100% irrigated i...

Palmer Amaranth (Amaranthus palmeri) Competition for Water in Cotton

Abstract Palmer amaranth is a troublesome weed in cotton production. Yield losses of 65% have been reported from season-long Palmer amaranth competition with cotton. To determine whether water is a factor in this system, experiments were conduced in 2011, 2012, and 2013 in Citra, FL, and in Tifton, GA. In 2011, infrequent rainfall lead to drought stress. The presence of Palmer amaranth resulted in decreased soil relative water content up to 1 m in depth. Cotton stomatal conductance (gs) was reduced up to 1.8 m from a Palmer amaranth plant. In 2012 and 2013 higher than average rainfall resulted in excess water throughout the growing season. In this situation, no differences were found in soil relative water content or cotton gs as a function of proximity to Palmer amaranth. A positive linear trend was found in cotton photosynthesis and yield; each parameter increased as distance from Palmer amaranth increased. Even in these well-watered conditions, daily water use of Palmer amaranth was considerably higher than that of cotton, at 1.2 and 0.49 g H20 cm−2 d−1, respectively. Although Palmer amaranth removed more water from the soil profile, rainfall was adequate to replenish the profile in 2 of the 3 yr of this study. However, yield loss due to Palmer amaranth was still observed despite no change in gs, indicating other factors, such as competition for light or response to neighboring plants during development, are driving yield loss. Nomenclature: Palmer amaranth, Amaranthus palmeri S. Wats.; cotton, Gossypium hirsutum L.

Reductions in a Commercial Potato Irrigation Schedule during Tuber Bulking in Florida: Physiological, Yield, and Quality Effects

Proper irrigation scheduling in potato (Solanum tuberosum L.) can lead to higher returns and more sustainable production practices when compared to systems that do not take plant water demand into account. In an attempt to reduce irrigation applications while minimizing yield reduction, we evaluated a novel deficit irrigation treatment utilizing a mild irrigation reduction during tuber bulking by comparing a typical commercial irrigation schedule to a partial irrigation schedule. Physiological, yield, and quality effects were quantified. Reducing the number of irrigation applications by 14 in 2011 and by 9 in 2012 minimally affected most parameters measured. However, a significant yield reduction of 11,713 kg/ha in the partial irrigation treatment occurred in 2011, likely because of the irrigation treatment commencing at the latter portion of tuber initiation. In 2012, the initiation of the partial irrigation was delayed and resulted in no significant difference in yield between the partial and full irrigation treatments. This study shows the potential for a reduced irrigation schedule for use by Florida potato growers as a sustainable option for potato production in this region.

Interaction of Tillage System and Irrigation Amount on Peanut Performance in the Southeastern U.S

Abstract A five-year study to investigate the potential interaction of conservation tillage with reduced irrigation amounts was conducted near Dawson, GA on peanut (Arachis hypogaea L.). Conventional tillage was compared to two conservation tillage programs (wide-strip and narrow-strip tillage) under four irrigation levels (100, 66, 33, and 0% of a recommended amount). Peanut yield did not exhibit a tillage by irrigation interaction as expected, although the main effects of irrigation and tillage were each significant by year due to weather variations. Peanut yield in narrow-strip tillage or wide-strip tillage were individually superior to conventional tillage in three seasons out of five, however only in one year did both conservation tillage systems outperform the conventional system. No detrimental effects on yields could be attributed to conservation tillage. Peanut quality and digging loss were dependent on the tillage by year effect as well as the main effect of irrigation. Irrigation increased tota...

Effects of Irrigation Method and Tillage Regime on Peanut (Arachis hypogaea L.) Reproductive Processes

The ability of peanut gynophores to peg through cover crop residue in reduced tillage systems is a primary concern of many growers and may be hindering adoption of the practice in peanut production. The interaction between tillage and irrigation could also play a major role in final yield. Experiments were conducted during 2004 and 2005 to determine what effects tillage (conventional tillage – CT and strip tillage – ST) and irrigation method (overhead – OH and subsurface drip – SDI) had on peanut reproductive processes and if climatic conditions were correlated with the formation of reproductive structures. Counts of flowers, pegs, and pods were conducted on two time scales: every 3–4 days for six weeks during peak flowering and peg production; and season long starting at 30 days after planting and continuing until harvest. In 2004, flowers were permanently tagged and the percent and time elapsed for peg production was measured. Overall, few differences in peanut reproduction between tillage treatments were found in either 2004 or 2005. The primary difference in reproduction was a greater production of flowers in ST than CT plants in 2004, but there were no subsequent differences in pod production due to the tillage system in that same year. The peak flowering time period in 2004 for both tillage and irrigation treatments was between 19 and 23 June, while in 2005, flower production peaked around 6 July. Maximum peg and pod counts in the OH and SDI irrigation treatments in both tillage treatments occurred between 4 July and 6 July 2005. There was a significant interaction for pod production between tillage and irrigation method in 2005 and showed, on average, the SDI-CT treatment produced 2.4 pods per plant in comparison to 1.5 pods per plant in the SDI-ST treatment, indicating that the use of the two management systems together be avoided. Limited effects of climatic conditions on formation of flowers, pegs and pods were found across all tillage and irrigation treatments in both years.

A high-throughput method to quantify root hair area in digital images taken in situ

Background and aimsRoot hair growth and development are important features of plant response to varying soil conditions and of nutrient and water uptake. Most current methods of characterizing root hairs in the field are unreliable or inefficient. We describe a method to quantify root hair area in digital images, such as those collected in situ by minirhizotron systems.MethodsThis method uses ImageJ and R open source software and is partially automated using code presented here. It requires manual tracing of a subset of root hair images (training data set) to which a multivariate logistic regression is fit with each color channel in the image as an independent variable. Thereafter the model is applied to complete sets of selected root hair sections to estimate total root hair area.ResultsThere was good agreement between the training data sets and the predictions of the regression models in castor (Ricinus communis L.), maize (Zea mays L.), and papaya (Carica papaya L.).ConclusionThis method enables time-efficient and consistent quantification of root hairs using in situ root imaging systems that are already widely in use.